Add Daisy Chain Protocol Documentation and instructions on how to build and flash

[mohamed-dek1]

Closes #153 and #163

Notes

Anything reviewers should be aware of when reviewing? Other related issues? Known problems? Future work?

Self-Review

1. Are all files under 300 kB (if not, please carefully assess whether it is worth committing them)? Yes
2. Are all files named according to the appropriate naming convention, i.e., dash-case, camelCase, snake case? Yes
3. Do all Markdown files follow the CONTRIBUTING article template? No
4. Do all links work in the material that the PR is adding? Yes
5. Is the PR configured to close the correct issue(s)? Yes
6. Did the PR fully address the Approach section of the issue(s) it is closing? Yes

Reviewer Instructions

Reviewers, please copy and paste a suitable review checklist into your review and answer all questions.

Appendix

This section should be the same for all PRs. Do not edit this section when creating a PR.

Review Checklists

Checklists maintained by the eLev lab for research repositories include:

• Report checklist
• Publication archive checklist (select a checklist from the Approach that corresponds to the step this PR seeks to complete).
• Standard checklist (if none of the above apply).

Standard checklist

1. Are all files under 300 kB (if not, please carefully assess whether it is worth committing them)? **Yes or No**
2. Are all files named according to the appropriate [naming convention](https://github.com/Severson-Group/research-repo-template?tab=readme-ov-file#file-naming), i.e., dash-case, camelCase, snake case? **Yes or No**
3. Do all Markdown files follow the [CONTRIBUTING article template](https://github.com/Severson-Group/.github/blob/main/CONTRIBUTING.md#markdown-documentation-template)? **Yes or No**
4. Do all links work in the material that the PR is adding? **Yes or No**
5. Is the PR configured to close the correct issue(s)? **Yes or No**
6. Did the PR fully address the `Approach` section of the issue(s) it is closing? **Yes or No**

Please work on addressing any **No** items.

[mohamed-dek1]

@elsevers, there is documentation on the Daisy Chain Protocol along with programming the AMDS. can you review this?

[elsevers]

To do:

• Update benchmark data for single AMDC-AMDS
  • Tracked here: #165
• On daisy chain page:
  • add daisy chain benchmark data (3x AMDS's with 8 cards each, 3x 2S boards with 2 cards each)
    • This comment provides links to where to find timing data and Saleae captures: Severson-Group/AMDS#102 (comment)
    • Tracked here: #167
  • remove discussion that reads like a diff
  • Explain a bit more on how it works (yes, discussion of DMA is good)
  • Cabling! Pinouts to wire it all up. What pins go to what pins.
    • Tracked here: #166
  • Explain how the header packets from each AMDS are adjusted as they progress through the chain and then what registers in the AMDC Firmware (AMDS_CH_1_DATA_REG_OFFSET - AMDS_CH_24_DATA_REG_OFFSET) they ultimately appear in.
    • Tracked here: #158

[elsevers]

Incomplete

[elsevers]

I have gone through this thoroughly, completing the minimum required to release this and splitting out other items into new issue. Let's merge this now into our next-release staging area.